<br><br><div class="gmail_quote">On Fri, May 18, 2012 at 1:27 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote"><div class="im">On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
I have no idea why you observe the dip, but it's probably irrelevant as you don't need a reaction coordinate that long, if this is the same plot that we've been discussing on the list.<br>
<br>
I must ask that you always post to the mailing list, for your own benefit, especially in the immediate future as I will be traveling for some time and will not reply very quickly to email; you stand a better chance getting help from others. I am also generally unable to dedicate much time debugging others' research on a personal level.<br>
<br>
-Justin<div><div><br></div></div></blockquote></div><div>Thank you Justin. I decreased the reaction coordinate and this dip still occurs:<br><br><a href="http://speedy.sh/2qHNa/Profile2.JPG" target="_blank">http://speedy.sh/2qHNa/Profile2.JPG</a><br>
<br>Its because of the applied weight of WHAM. Any suggestions please?<br><br>Steven<br></div></div></blockquote><div><br>Hi Justin,<br><br>I run umbrella sampling of my ligand binding to different part of my residues. Each time my PMF profile is smooth but at the end the small dip occurs. Here another example:<br>
<br><a href="http://speedy.sh/dbUg9/ProfileHA1.JPG">http://speedy.sh/dbUg9/ProfileHA1.JPG</a><br><br><a href="http://speedy.sh/8zZ52/HistoHA1.JPG">http://speedy.sh/8zZ52/HistoHA1.JPG</a><br><br>What can be causing this? Shall I just igonore this taking the plateau value or run a longer simulations in each window?<br>
<br>Best,<br><br>Steven<br><br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div><div class="im">
<br>
On 5/18/12 4:17 AM, Steven Neumann wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin,<br>
<br>
<br><div class="im">
I run umbrella sampling (pulling ligand away from the protein) simulations to<br>
get deltaG:<br>
<br>
<a href="http://speedy.sh/XpUks/Profile.JPG" target="_blank">http://speedy.sh/XpUks/<u></u>Profile.JPG</a><br>
<br>
<a href="http://speedy.sh/yvJKx/Histogram.JPG" target="_blank">http://speedy.sh/yvJKx/<u></u>Histogram.JPG</a><br>
<br>
I know I need one more window around 1 nm but apart from this histrogram looks<br>
really good. My each window was 50 ns.<br>
<br>
Why the plateau in the end goes down of 0.4 kcal/mol? Would you suggest longer<br>
simulation in each window?<br>
<br>
Thank you and sorry for writing straight to your email,<br>
<br>
Best<br>
<br>
Steven<br>
<br>
<br>
</div></blockquote>
<br></div></div><div class="im"><span><font color="#888888">
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Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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